We have a set of images which are immunofluorescence stainings of mice brain slices. These image show the expression level of a marked protein.

We have two groups of mice, which underwent behavioral experiments that we suspect caused a change in the expression of this protein.

So we want to compare the signal intensity between this two groups of images. Which could be the better approach?

We thought of taking the luminosity channel of every pixel in the selected area and average it among all the pixel to retrieve a single luminosity value for the picture. Is this a correct method? Isn't it too much simple? Is there a better method to achieve more significant data?